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Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to…
Coarse-grained molecular dynamics often sacrifices accuracy and transferability for computational efficiency, but the use of machine learned potentials is helping coarse-grained models attain performance on par with atomistic molecular…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…
Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new…
We propose a new Cahn-Hilliard phase field model coupled to incompressible viscoelasticity at large strains, obtained from a diffuse interface mixture model and formulated in the Eulerian configuration. A new kind of diffusive…
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review…
3D action recognition was shown to benefit from a covariance representation of the input data (joint 3D positions). A kernel machine feed with such feature is an effective paradigm for 3D action recognition, yielding state-of-the-art…
Even though atomistic and coarse-grained (CG) models have been used to simulate liquid nanodroplets in vapor, very few rigorous studies of the liquid-liquid interface structure are available, and most of them are limited to planar…
Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
In this contribution, a novel framework for simulating mixed-mode failure in rock is presented. Based on a hybrid phase-field model for mixed-mode fracture, separate phase-field variables are introduced for tensile (mode I) and shear (mode…
Noncovalent interactions--vdW dispersion, hydrogen/halogen bonding, ion-$\pi$, and $\pi$-stacking--govern structure, dynamics, and emergent phenomena in materials and molecular systems, yet accurately learning them alongside covalent forces…
We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high…
Although molten carbonates only represent, at most, a very minor phase in the Earth's mantle, they are thought to be implied in anomalous high-conductivity zones in its upper part (70-350 km). Besides the high electrical conductivity of…
The $\xi$-based spatially adaptive three-field variable phase-field model for quasi-static anti-plane crack propagation is introduced. A dynamically optimized regularization length is integrated to improve computational efficiency and…